Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Kalhoefer, Daniela ^a   Thole, Sebastian ^a   Voget, Sonja ^b   Lehmann, Rüdiger ^b   Liesegang, Heiko ^b   Wollher, Antje ^b   Daniel, Rolf ^b   Simon, Meinhard ^a   Brinkhoff, Thorsten ^a  

^a UNIVERSITY OF OLDENBURG   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN; SUGAR; ZINC; GLYCOGEN; HEAVY METAL;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; CARBON METABOLISM; CATABOLISM; CLADISTICS; CONTROLLED STUDY; GENE FUNCTION; GENE LOCATION; GENE REARRANGEMENT; GENE TRANSFER; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC DIFFERENCE; GENOME ANALYSIS; GENOMIC ISLAND; HEAVY METAL RESISTANCE GENE; HOST RANGE; NONHUMAN; PHOTOSYNTHESIS; PHOTOSYNTHESIS GENE; PLASMID; ROSEOBACTER; ROSEOBACTER DENITRIFICANS; ROSEOBACTER LITORALIS; SPECIES DIFFERENCE; TYPE STRAIN; CHEMISTRY; COMPARATIVE STUDY; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY;

ALGAE; ROSEOBACTER; ROSEOBACTER DENITRIFICANS; ROSEOBACTER LITORALIS;

GENOME, BACTERIAL; GENOMIC ISLANDS; GLYCOGEN; METALS, HEAVY; MOLECULAR SEQUENCE DATA; PHOTOSYNTHESIS; PLASMIDS; ROSEOBACTER; SPECIES SPECIFICITY;

EID: 79959228028     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-324     Document Type: Article

References (96)

1. Shiba T. Roseobacter litoralis gen. nov., sp. nov, and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll-a. Syst Appl Microbiol 1991, 14:140-145.
2. Shioi Y, Doi M, Arata H, Takamiya K. A denitrifying activity in an aerobic photosynthetic bacterium, Erythrobacter sp. strain Och 114. Plant Cell Physiol 1988, 29:861-865.
3. Arata H, Serikawa Y, Takamiya K. Trimethylamine N-oxide respiration by aerobic photosynthetic bacterium, Erythrobacter sp. OCh 114. J Biochem 1988, 103:1011-1015.
4. Holert J, Hahnke S, Cypionka H. Influence of light and anoxia on chemiosmotic energy conservation in Dinoroseobacter shibae. Environ Microbiol Rep 2010,
5. Pradella S, Allgaier M, Hoch C, Pauker O, Stackebrandt E, Wagner-Doebler I. Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 2004, 70:3360-3369. 10.1128/AEM.70.6.3360-3369.2004, 427745, 15184132.
6. Brinkhoff T, Giebel HA, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 2008, 189:531-539. 10.1007/s00203-008-0353-y, 18253713.
7. Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H, Acharya CR, Conrad AL, Taylor HL, Dejesa LC, Shah MK, O'Huallachain ME, Lince MT, Blankenship RE, Beatty JT, Touchman JW. The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 2007, 189:683-690. 10.1128/JB.01390-06, 1797316, 17098896.
8. Silver S. Bacterial resistances to toxic metal ions - a review. Gene 1996, 179:9-19. 10.1016/S0378-1119(96)00323-X, 8991852.
9. Silver S, Phung LT. Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 1996, 50:753-789. 10.1146/annurev.micro.50.1.753, 8905098.
10. Altug G, Balkis N. Levels of some toxic elements and frequency of bacterial heavy metal resistance in sediment and sea water. Environ Monit and Assess 2009, 149:61-69.
11. Toes ACM, Finke N, Kuenen JG, Muyzer G. Effects of deposition of heavy-metal-polluted harbor mud on microbial diversity and metal resistance in sandy marine sediments. Arch of Environ Contam Tox 2008, 55:372-385.
12. Al-Homaidan AA. Heavy metal concentrations in three species of green algae from the Saudi coast of the Arabian Gulf. J Food Agric Environ 2007, 5:354-358.
13. Kalesh NS, Nair SM. Spatial and temporal variability of copper, zinc, and cobalt in marine macroalgae from the southwest coast of India. Bull Environ Contam Toxicol 2006, 76:293-300. 10.1007/s00128-006-0920-3, 16468009.
14. Hamdy AA. Biosorption of heavy metals by marine algae. Curr Microbiol 2000, 41:232-238. 10.1007/s002840010126, 10977888.
15. Klerks PL, Weis JS. Genetic adaptation to heavy metals in aquatic organisms - a review. Environ Pollut 1987, 45:173-205. 10.1016/0269-7491(87)90057-1, 15092750.
16. Petersen J, Brinkmann H, Pradella S. Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 2009, 11:2627-2638. 10.1111/j.1462-2920.2009.01987.x, 19601964.
17. Osborn AM, Boeltner D. When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Plasmid 2002, 48:202-212. 10.1016/S0147-619X(02)00117-8, 12460536.
18. Dobrindt U, Hochhut B, Hentschel U, Hacker J. Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2:414-424. 10.1038/nrmicro884, 15100694.
19. Mira A, Martin-Cuadrado AB, D'Auria G, Rodriguez-Valera F. The bacterial pan-genome: a new paradigm in microbiology. Int Microbiol 2010, 13:45-57.
20. Richardson JS, Hynes MF, Oresnik IJ. A genetic locus necessary for rhamnose uptake and catabolism in Rhizobium leguminosarum bv. trifolii. J Bacteriol 2004, 186:8433-8442. 10.1128/JB.186.24.8433-8442.2004, 532407, 15576793.
21. Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A. Ecological genomics of marine roseobacters. Appl Environ Microbiol 2007, 73:4559-4569. 10.1128/AEM.02580-06, 1932822, 17526795.
22. Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, Howard EC, King E, Oakley CA, Reisch CR, Rinta-Kanto JM, Sharma S, Sun SL, Varaljay V, Vila-Costa M, Westrich JR, Moran MA. Genome characteristics of a generalist marine bacterial lineage. ISME J 2010, 4:784-798. 10.1038/ismej.2009.150, 20072162.
23. Tang K, Huang HZ, Jiao NZ, Wu CH. Phylogenomic analysis of marine Roseobacters. PLoS One 2010, 5:e11604. 10.1371/journal.pone.0011604, 2904699, 20657646.
24. Cunliffe M. Correlating carbon monoxide oxidation with cox genes in the abundant marine Roseobacter clade. ISME J 2010,
25. Godfroid F, Taminiau B, Danese I, Denoel P, Tibor A, Weynants V, Cloeckaert A, Godfroid J, Letesson JJ. Identification of the perosamine synthetase gene of Brucella melitensis 16 M and involvement of lipopolysaccharide O side chain in Brucella survival in mice and in macrophages. Infect Immun 1998, 66:5485-5493. 108687, 9784561.
26. Pena A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverria J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C, Dossat C, Barbe V, Dopazo J, Rossello-Mora R, Schuler M, Glockner FO, Amann R, Gabaldon T, Anton J. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J 2010, 4:882-895. 10.1038/ismej.2010.6, 20164864.
27. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R. Microbiology in the post-genomic era. Nat Rev Microbiol 2008, 6:419-430.
28. Huang C, Zhang Y, Jiao N. Phage resistance of a marine bacterium, Roseobacter denitrificans OCh114, as revealed by comparative proteomics. Curr Microbiol 2010,
29. Nies DH. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev 2003, 27:313-339. 10.1016/S0168-6445(03)00048-2, 12829273.
30. Grass G, Fan B, Rosen BP, Franke S, Nies DH, Rensing C. ZitB (YbgR), a member of the cation diffusion facilitator family, is an additional zinc transporter in Escherichia coli. J Bacteriol 2001, 183:4664-4667. 10.1128/JB.183.15.4664-4667.2001, 95364, 11443104.
31. Ullrich S, Kube M, Schubbe S, Reinhardt R, Schuler D. A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. J Bacteriol 2005, 187:7176-7184. 10.1128/JB.187.21.7176-7184.2005, 1272989, 16237001.
32. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk HP, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, von Jan M, Wanphrut N, Wichels A, Zech H, Simon M. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 2010, 4:61-77. 10.1038/ismej.2009.94, 19741735.
33. Geddes BA, Pickering BS, Poysti NJ, Collins H, Yudistira H, Oresnik IJ. A locus necessary for the transport and catabolism of erythritol in Sinorhizobium meliloti. Microbiology 2010, 156:2970-2981. 10.1099/mic.0.041905-0, 20671019.
34. Yost CK, Rath AM, Noel TC, Hynes MF. Characterization of genes involved in erythritol catabolism in Rhizobium leguminosarum bv. viciae. Microbiology 2006, 152:2061-2074. 10.1099/mic.0.28938-0, 16804181.
35. Gonzalez V, Bustos P, Ramirez-Romero MA, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodriguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Davila G. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol 2003, 4:R36. 10.1186/gb-2003-4-6-r36, 193615, 12801410.
36. Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000, 1:research00111-00119.
37. Whitfield C. Biosynthesis of lipopolysaccharide O-antigens. Trends Microbiol 1995, 3:178-185. 10.1016/S0966-842X(00)88917-9, 7542987.
38. The IMG Database. , http://img.jgi.doe.gov/cgi-bin/w/main.cgi
39. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao XL, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. The integrated microbial genomes (IMG) system. Nucleic Acids Res 2006, 34:D344-D348. 10.1093/nar/gkj024, 1347387, 16381883.
40. Biebl H, Wagner-Döbler I. Growth and bacteriochlorophyll-a formation in taxonomically diverse aerobic anoxygenic phototrophic bacteria in chemostat culture: Influence of light regimen and starvation. Process Biochem 2006, 41:2153-2159.
41. Igarashi N, Harada J, Nagashima S, Matsuura K, Shimada K, Nagashima KVP. Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J Mol Evol 2001, 52:333-341.
42. Yutin N, Beja O. Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics. Environ Microbiol 2005, 7:2027-2033. 10.1111/j.1462-2920.2005.00843.x, 16309398.
43. Barabote RD, Saier MH. Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev 2005, 69:608-634. 10.1128/MMBR.69.4.608-634.2005, 1306802, 16339738.
44. Postma PW, Lengeler JW, Jacobson GR. Phosphoenolpyruvate - carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 1993, 57:543-594. 372926, 8246840.
45. Gonzalez CF, Stonestrom AJ, Lorca GL, Saier MH. Biochemical characterization of phosphoryl transfer involving HPr of the phosphoenolpyruvate-dependent phosphotransferase system in Treponema denticola, an organism that lacks PTS permeases. Biochemistry 2005, 44:598-608. 10.1021/bi048412y, 15641785.
46. Pinedo CA, Bringhurst RM, Gage DJ. Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production. J Bacteriol 2008, 190:2947-2956. 10.1128/JB.01917-07, 2293241, 18281401.
47. De Ley J, Doudoroff M. The metabolism of D-galactose in Pseudomonas saccharophila. J Biol Chem 1957, 227:745-757.
48. Watanabe S, Kodak T, Makino K. Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism. J Biol Chem 2006, 281:2612-2623.
49. Watanabe S, Kodaki T, Makino K. A novel alpha-ketoglutaric semialdehyde dehydrogenase - Evolutionary insight into an alternative pathway of bacterial L-arabinose metabolism. J Biol Chem 2006, 281:28876-28888. 10.1074/jbc.M602585200, 16835232.
50. Watanabe S, Shimada N, Tajima K, Kodaki T, Makino K. Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism - Novel evolutionary insight into sugar metabolism. J Biol Chem 2006, 281:33521-33536. 10.1074/jbc.M606727200, 16950779.
51. Van Bastelaere E, Lambrecht M, Vermeiren H, Van Dommelen A, Keijers V, Proost P, Vanderleyden J. Characterization of a sugar-binding protein from Azospirillum brasilense mediating chemotaxis to and uptake of sugars. Mol Microbiol 1999, 32:703-714. 10.1046/j.1365-2958.1999.01384.x, 10361275.
52. Doty SL, Chang M, Nester EW. The chromosomal virulence gene, chvE, of Agrobacterium tumefaciens is regulated by a LysR family member. J Bacteriol 1993, 175:7880-7886. 206966, 8253677.
53. Kemner JM, Liang X, Nester EW. The Agrobacterium tumefaciens virulence gene chvE is part of a putative ABC-type sugar transport operon. J Bacteriol 1997, 179:2452-2458. 178989, 9079938.
54. Ankenbauer RG, Nester EW. Sugar-mediated induction of Agrobacterium tumefaciens virulence genes - structural specificity and activities of monosaccharides. J Bacteriol 1990, 172:6442-6446. 526831, 2121715.
55. Zhu Y, Lin EC. An evolvant of Escherichia coli that employs the L-fucose pathway also for growth on L-galactose and D-arabinose. J Mol Evol 1986, 23:259-266. 10.1007/BF02115582, 3100814.
56. Asada Y, Endo S, Inoue Y, Mamiya H, Hara A, Kunishima N, Matsunaga T. Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8: a hyperthermostable aldose-1-dehydrogenase with broad substrate specificity. Chem Biol Interact 2009, 178:117-126. 10.1016/j.cbi.2008.09.018, 18926808.
57. Bourassa L, Camilli A. Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae. Mol Microbiol 2009, 72:124-138. 10.1111/j.1365-2958.2009.06629.x, 2704980, 19226328.
58. Ugalde JE, Parodi AJ, Ugalde RA. De novo synthesis of bacterial glycogen Agrobacterium tumefaciens glycogen synthase is involved in glucan initiation and elongation. Proc Natl Acad Sci USA 2003, 100:10659-10663. 10.1073/pnas.1534787100, 196860, 12960388.
59. Zevenhuizen LPTM. Cellular glycogen, beta-1,2-glucan, poly-beta-hydroxybutyric acid and extracellular polysaccharides in fast-growing species of Rhizobium. Antonie Van Leeuwenhoek 1981, 47:481-497. 10.1007/BF00443236, 7337433.
60. Fürch T, Preusse M, Tomasch J, Zech H, Wagner-Doebler I, Rabus R, Wittmann C. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BMC Microbiol 2009, 9:209. 10.1186/1471-2180-9-209, 2761930, 19788729.
61. Zech H, Thole S, Schreiber K, Kalhofer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R. Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 2009, 9:3677-3697. 10.1002/pmic.200900120, 19639587.
62. The InterPro Database. , http://www.ebi.ac.uk/interpro/
63. Garrow TA. Purification, kinetic properties, and cDNA cloning of mammalian betaine-homocysteine methyltransferase. J Biol Chem 1996, 271:22831-22838.
64. The Uniprot Database. , http://www.uniprot.org/uniprot
65. Barra L, Fontenelle C, Ermel G, Trautwetter A, Walker GC, Blanco C. Interrelations between glycine betaine catabolism and methionine biosynthesis in Sinorhizobium meliloti strain 102F34. J Bacteriol 2006, 188:7195-7204. 10.1128/JB.00208-06, 1636217, 17015658.
66. Cook AM, Denger K. Metabolism of taurine in microorganisms: a primer in molecular biodiversity?. Adv Exp Med Biol 2006, 583:3-13. 10.1007/978-0-387-33504-9_1, 17153584.
67. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll-a. Int J Syst Bacteriol 1982, 32:211-217.
68. Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lunsdorf H, Pukall R, Wagner-Dobler I. Dinoroseobacter shibae gen. nov., sp nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. Int J Syst Evol Microbiol 2005, 55:1089-1096. 10.1099/ijs.0.63511-0, 15879238.
69. Bamforth CW, Quayle JR. Aerobic and anaerobic growth of Paracoccus denitrificans on methanol. Arch Microbiol 1978, 119:91-97. 10.1007/BF00407934, 718372.
70. Pasternak C, Assemat K, Clement-Metral JD, Klug G. Thioredoxin is essential for Rhodobacter sphaeroides growth by aerobic and anaerobic respiration. Microbiology 1997, 143(Pt 1):83-91.
71. Shearer N, Hinsley AP, Van Spanning RJ, Spiro S. Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes. J Bacteriol 1999, 181:6907-6913. 94164, 10559155.
72. Sfriso A, Pavoni B, Marcomini A, Orio AA. Macroalgae, nutrient cycles, and pollutants in the Lagoon of Venice. Estuaries 1992, 15:517-528.
73. The Microbial Genome Sequencing Project. , http://camera.calit2.net/microgenome/
74. The Staden Package. , http://staden.sourceforge.net/
75. Tech M, Merkl R. YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol 2003, 3:441-451.
76. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis comparison tool. Bioinformatics 2005, 21:3422-3423. 10.1093/bioinformatics/bti553, 15976072.
77. Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. The ERGO (TM) genome analysis and discovery system. Nucleic Acids Res 2003, 31:164-171. 10.1093/nar/gkg148, 165577, 12519973.
78. The ExPASy Proteomics Server. , http://kr.expasy.org/
79. Zdobnov EM, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
80. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120. 10.1093/bioinformatics/btn578, 2612626,2612626, 18990721.
81. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403. 10.1101/gr.2289704, 442156, 15231754.
82. Langille MGI, Brinkman FSL. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665. 10.1093/bioinformatics/btp030, 2647836, 19151094.
83. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7:142. 10.1186/1471-2105-7-142, 1489950, 16542435.
84. Rocha EP. The organization of the bacterial genome. Annu Rev Genet 2008, 42:211-233. 10.1146/annurev.genet.42.110807.091653, 18605898.
85. Hiller K, Grote A, Scheer M, Munch R, Jahn D. PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res 2004, 32:W375-W379. 10.1093/nar/gkh378, 441516, 15215414.
86. Puigbò P, Bravo IG, Garcia-Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 2008, 3:38. 10.1186/1745-6150-3-38, 2553769, 18796141.
87. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
88. Karp PD, Riley M, Paley SM, Pellegrini-Toole A. The MetaCyc database. Nucleic Acids Res 2002, 30:59-61. 10.1093/nar/30.1.59, 99148, 11752254.
89. Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, Paley SM, Pellegrini-Toole A, Bonavides C, Gama-Castro S. The EcoCyc database. Nucleic Acids Res 2002, 30:56-58. 10.1093/nar/30.1.56, 99147, 11752253.
90. The BioCyc Database Collection. , http://biocyc.org/
91. Shioi Y. Growth characteristics and substrate specificity of aerobic photosynthetic bacterium, Erythrobacter sp. (Och 114). Plant Cell Physiol 1986, 27:567-572.
92. Geng H, Bruhn JB, Nielsen KF, Gram L, Belas R. Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. Appl Environ Microbiol 2008, 74:1535-1545. 10.1128/AEM.02339-07, 2258615, 18192410.
93. Wagner-Döbler I, Rheims H, Felske A, Pukall R, Tindall BJ. Jannaschia helgolandensis gen. nov., sp nov., a novel abundant member of the marine Roseobacter clade from the North Sea. Int J Syst Evol Micr 2003, 53:731-738.
94. Wagner-Döbler I, Rheims H, Felske A, El-Ghezal A, Flade-Schorder D, Laatsch H, Lang S, Pukall R, Tindall BJ. Oceanibulbus indolifex gen. nov., sp nov., a North Sea alphaproteobacterium that produces bioactive metabolites. Int J Syst Evol Micr 2004, 54:1177-1184.
95. The Marine Microbiology Initiative of the Moore Foundation. , http://www.moore.org/marine-micro.aspx
96. The NCBI Database. , http://www.ncbi.nlm.nih.gov/